{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:35Z","timestamp":1772138075932,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: The solution of high-dimensional inference and prediction problems in computational biology is almost always a compromise between mathematical theory and practical constraints, such as limited computational resources. As time progresses, computational power increases but well-established inference methods often remain locked in their initial suboptimal solution.<\/jats:p>\n                  <jats:p>Results: We revisit the approach of Segal et al. to infer regulatory modules and their condition-specific regulators from gene expression data. In contrast to their direct optimization-based solution, we use a more representative centroid-like solution extracted from an ensemble of possible statistical models to explain the data. The ensemble method automatically selects a subset of most informative genes and builds a quantitatively better model for them. Genes which cluster together in the majority of models produce functionally more coherent modules. Regulators which are consistently assigned to a module are more often supported by literature, but a single model always contains many regulator assignments not supported by the ensemble. Reliably detecting condition-specific or combinatorial regulation is particularly hard in a single optimum but can be achieved using ensemble averaging.<\/jats:p>\n                  <jats:p>Availability: All software developed for this study is available from http:\/\/bioinformatics.psb.ugent.be\/software.<\/jats:p>\n                  <jats:p>Contact: \u00a0tom.michoel@psb.ugent.be<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data and figures are available from http:\/\/bioinformatics.psb.ugent.be\/supplementary_data\/anjos\/module_nets_yeast\/.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn658","type":"journal-article","created":{"date-parts":[[2009,1,9]],"date-time":"2009-01-09T20:34:33Z","timestamp":1231533273000},"page":"490-496","source":"Crossref","is-referenced-by-count":76,"title":["Module networks revisited: computational assessment and prioritization of model predictions"],"prefix":"10.1093","volume":"25","author":[{"given":"Anagha","family":"Joshi","sequence":"first","affiliation":[{"name":"1 Department of Plant Systems Biology, VIB, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Gent, 3CMPG, Department of Microbial and Molecular Systems, KULeuven, Kasteelpark Arenberg 20 and 4ESAT-SCD, KULeuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium"},{"name":"1 Department of Plant Systems Biology, VIB, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Gent, 3CMPG, Department of Microbial and Molecular Systems, KULeuven, Kasteelpark Arenberg 20 and 4ESAT-SCD, KULeuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Riet","family":"De Smet","sequence":"additional","affiliation":[{"name":"1 Department of Plant Systems Biology, VIB, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Gent, 3CMPG, Department of Microbial and Molecular Systems, KULeuven, Kasteelpark Arenberg 20 and 4ESAT-SCD, KULeuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kathleen","family":"Marchal","sequence":"additional","affiliation":[{"name":"1 Department of Plant Systems Biology, VIB, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Gent, 3CMPG, Department of Microbial and Molecular Systems, KULeuven, Kasteelpark Arenberg 20 and 4ESAT-SCD, KULeuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium"},{"name":"1 Department of Plant Systems Biology, VIB, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Gent, 3CMPG, Department of Microbial and Molecular Systems, KULeuven, Kasteelpark Arenberg 20 and 4ESAT-SCD, KULeuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yves","family":"Van de Peer","sequence":"additional","affiliation":[{"name":"1 Department of Plant Systems Biology, VIB, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Gent, 3CMPG, Department of Microbial and Molecular Systems, KULeuven, Kasteelpark Arenberg 20 and 4ESAT-SCD, KULeuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium"},{"name":"1 Department of Plant Systems Biology, VIB, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Gent, 3CMPG, Department of Microbial and Molecular Systems, KULeuven, Kasteelpark Arenberg 20 and 4ESAT-SCD, KULeuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom","family":"Michoel","sequence":"additional","affiliation":[{"name":"1 Department of Plant Systems Biology, VIB, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Gent, 3CMPG, Department of Microbial and Molecular Systems, KULeuven, Kasteelpark Arenberg 20 and 4ESAT-SCD, KULeuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium"},{"name":"1 Department of Plant Systems Biology, VIB, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Gent, 3CMPG, Department of Microbial and Molecular Systems, KULeuven, Kasteelpark Arenberg 20 and 4ESAT-SCD, KULeuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,1,9]]},"reference":[{"key":"2023013110095878400_B1","doi-asserted-by":"crossref","first-page":"17559","DOI":"10.1073\/pnas.0509033102","article-title":"Reconstructing the pathways of a cellular system from genome-scale signals by using matrix and tensor computations","volume":"102","author":"Alter","year":"2005","journal-title":"Proc. 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